4ZXH

Crystal Structure of holo-AB3403 a four domain nonribosomal peptide synthetase from Acinetobacter Baumanii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of two distinct conformations of holo-non-ribosomal peptide synthetases.

Drake, E.J.Miller, B.R.Shi, C.Tarrasch, J.T.Sundlov, J.A.Allen, C.L.Skiniotis, G.Aldrich, C.C.Gulick, A.M.

(2016) Nature 529: 235-238

  • DOI: 10.1038/nature16163
  • Primary Citation of Related Structures:  4ZXI, 4ZXJ
  • Also Cited By: 5JA1, 5JA2

  • PubMed Abstract: 
  • Many important natural products are produced by multidomain non-ribosomal peptide synthetases (NRPSs). During synthesis, intermediates are covalently bound to integrated carrier domains and transported to neighbouring catalytic domains in an assembly ...

    Many important natural products are produced by multidomain non-ribosomal peptide synthetases (NRPSs). During synthesis, intermediates are covalently bound to integrated carrier domains and transported to neighbouring catalytic domains in an assembly line fashion. Understanding the structural basis for catalysis with non-ribosomal peptide synthetases will facilitate bioengineering to create novel products. Here we describe the structures of two different holo-non-ribosomal peptide synthetase modules, each revealing a distinct step in the catalytic cycle. One structure depicts the carrier domain cofactor bound to the peptide bond-forming condensation domain, whereas a second structure captures the installation of the amino acid onto the cofactor within the adenylation domain. These structures demonstrate that a conformational change within the adenylation domain guides transfer of intermediates between domains. Furthermore, one structure shows that the condensation and adenylation domains simultaneously adopt their catalytic conformations, increasing the overall efficiency in a revised structural cycle. These structures and the single-particle electron microscopy analysis demonstrate a highly dynamic domain architecture and provide the foundation for understanding the structural mechanisms that could enable engineering of novel non-ribosomal peptide synthetases.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABBFA_003403
A
1320Acinetobacter baumannii (strain AB307-0294)N/A
Find proteins for A0A0X1KH98 (Acinetobacter baumannii (strain AB307-0294))
Go to UniProtKB:  A0A0X1KH98
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PNS
Query on PNS

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Download CCD File 
A
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
PX4
Query on PX4

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Download CCD File 
A
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 116.187α = 90.00
b = 116.187β = 90.00
c = 348.607γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALAdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM068440
US Army Medical Research and Materiel CommandUnited StatesW81XWH-11-2-0218

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2016-02-17
    Type: Refinement description
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Derived calculations